Valentin Barberoux, Adriana Anzil, Loïc Meinertzhagen, Thanh Nguyen-Dinh, Pierre Servais, Isabelle F George
{"title":"Spatio-temporal dynamics of bacterial community composition in a Western European watershed, the Meuse River watershed.","authors":"Valentin Barberoux, Adriana Anzil, Loïc Meinertzhagen, Thanh Nguyen-Dinh, Pierre Servais, Isabelle F George","doi":"10.1093/femsec/fiaf022","DOIUrl":"10.1093/femsec/fiaf022","url":null,"abstract":"<p><p>This study aimed to identify factors influencing bacterial diversity in the Meuse River watershed by analyzing 42 locations sampled in spring and summer 2019, combined with biweekly sampling of one mid-stream location for a year. Bacterial community composition (BCC) was assessed in the small (SF; <5 µm) and large fractions (LF; ≥5 µm,), alongside physico-chemical parameters. LF consistently exhibited greater alpha diversity than SF. During the spatial campaigns, alpha diversity increased downstream in spring with high discharge, and BCC differed significantly between headwaters and the main river. Along this axis, several genera, Flavobacterium, Limnohabitans, and Aquirufa stood out as indicators of good water quality. Rhodoferax, another taxon indicative of good water quality, prevailed in the headwaters and during winter. In contrast, two cyanobacteria genera indicators of poor river quality, Microcystis PCC 7914 and Cyanobium PCC 6307, peaked in summer. BCC in spring and summer temporal samples aligned with spatial ones, while winter and autumn samples had distinct BCC. Finally, season, temperature, and distance from river mouth were the main driving parameters of beta diversity, outweighing the effect of fraction size on the BCC. These findings reinforce the notion that local conditions exert significant influence on bacterial communities in rivers.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11916896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143566530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Plipastatin is a shared good by Bacillus subtilis during combating Fusarium spp.","authors":"Rune Overlund Stannius, Ákos T Kovács","doi":"10.1093/femsec/fiaf020","DOIUrl":"10.1093/femsec/fiaf020","url":null,"abstract":"<p><p>Bacillus subtilis a Gram-positive soil-dwelling bacterium known for its wide range of bioactive secondary metabolites. The lipopeptide plipastatin produced by most B. subtilis isolates have been shown to exhibit potent antifungal activity against plant pathogenic fungi. While the effect of these antifungal compounds are well studied in the context of biocontrol, much less is known of their role in the environment, which also harbor nonproducing strains of these compounds. Fusarium species produce multiple antibacterial compounds resulting in dysbiosis of the plant-associated microbiome and inhibition of plant beneficial bacteria like B. subtilis. While plipastatin is expected to be important for survival of B. subtilis, not all isolates carry the biosynthetic gene cluster for plipastatin suggesting that the protective effect of plipastatin might be shared. In this study, we investigated the protective effect of plipastatin against Fusarium oxysporum in a coculture using a producer and a nonproducer isolate of plipastatin. We tested the survival of single and cocultured strains under Fusarium challenge in liquid media and solid agar plates to dissect the influence of spatial structure. Our results highlights that plipastatin protects the nonproducer strain in a density-dependent manner.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11916886/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Giuliano Bonanomi, Giuseppina Iacomino, Luigi Di Costanzo, Mauro Moreno, Giulio Tesei, Marina Allegrezza, Stefano Mazzoleni, Mohamed Idbella
{"title":"Mechanisms and impacts of Agaricus urinascens fairy rings on plant diversity and microbial communities in a montane Mediterranean grassland.","authors":"Giuliano Bonanomi, Giuseppina Iacomino, Luigi Di Costanzo, Mauro Moreno, Giulio Tesei, Marina Allegrezza, Stefano Mazzoleni, Mohamed Idbella","doi":"10.1093/femsec/fiaf034","DOIUrl":"10.1093/femsec/fiaf034","url":null,"abstract":"<p><p>Fungal fairy rings (FFRs) significantly influence plant communities and soil microbiota. This study investigated the development of Agaricus urinascens fairy rings in a species-rich montane Mediterranean grassland. By combining vegetation analysis, soil chemistry measurements, and next-generation sequencing, we assessed fairy rings' impact on soil properties, plants, fungi, and bacteria. Our findings reveal a fungal-driven transformation of biological communities, with significant variations across FFRs zones. At the fungal front (FF), plant biomass decreased slightly but increased more than threefold inside the ring (>1100 g m-2), favouring grasses like Brachypodium genuense over forbs. In addition, species richness dropped significantly in the FF (-40%) compared to surrounding grassland, particularly affecting perennials. Moreover, our findings reveal substantial alterations in soil properties at the FF, including a 534% increase in P₂O5, a 210% rise in electrical conductivity, and a 36% increase in soil hydrophobicity compared to the surrounding grassland. Clay content at the FF was nearly three times higher than outside the ring (162.8 versus 57.5 g kg-1), indicating potential structural modifications in the soil matrix. Organic carbon decreased by 10% in the FF, while the C/N ratio and cation exchange capacity dropped significantly. Distinct shifts in microbial composition were observed. Bacterial diversity declined at the FF, where Actinobacteria dominated (85%) and Proteobacteria dropped to 8%. Similarly, fungal diversity was lowest inside the ring but highest in the belt section, with Ascomycota reaching 97% at the FF. Certain taxa, such as Kribbella, Streptomyces, Trichoderma, Penicillium, and Dichotomopilus, coexisted with A. urinascens mycelium. Notably, hydrophobicity at the FF was linked to high calcium oxalate crystal coverage on fungal mycelium and plant roots. This may have accelerated root desiccation, ultimately leading to plant mortality. Overall, our findings provide strong evidence that fairy ring fungi act as ecosystem engineers, shaping the spatial patterns of biotic composition and diversity in Mediterranean grasslands.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11983688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dominika Klimek, Malte Herold, Inês Rosado Vitorino, Zuzana Dedova, Sebastien Lemaigre, Jimmy Roussel, Xavier Goux, Olga Maria Lage, Magdalena Calusinska
{"title":"Insights into the phylogenetic and metabolic diversity of Planctomycetota in anaerobic digesters and the isolation of novel Thermoguttaceae species.","authors":"Dominika Klimek, Malte Herold, Inês Rosado Vitorino, Zuzana Dedova, Sebastien Lemaigre, Jimmy Roussel, Xavier Goux, Olga Maria Lage, Magdalena Calusinska","doi":"10.1093/femsec/fiaf025","DOIUrl":"10.1093/femsec/fiaf025","url":null,"abstract":"<p><p>Studying bacteria in anaerobic digestion (AD) is crucial for optimizing microbial processes. While abundant taxa are often studied, less abundant groups may harbour novel metabolic potential. This study fills the gap by focusing on the Planctomycetota phylum, known to encode diverse carbohydrate-active enzymes (CAZymes). Despite their common presence in diverse aerobic and anaerobic environments, their role in AD is relatively unexplored. We utilized both culture-dependent and culture-independent techniques to investigate the phylogenetic and metabolic diversity of Planctomycetota within AD reactors. Our findings revealed that among the diverse planctomycetotal operational taxonomic units present, only a few are prevalent and abundant community members. Planctomycetota share functional traits with e.g. Verrucomicrobiota exhibiting distinct CAZyme gene repertoires that indicates specialization in degrading algal polysaccharides and glycoproteins. To explore the planctomycetotal metabolic capabilities, we monitored their presence in algal-fed digesters. Additionally, we isolated a strain from mucin-based medium, revealing its genetic potential for a mixotrophic lifestyle. Based on the genomic analysis, we propose to introduce the Candidatus Luxemburgiella decessa gen. nov. sp. nov., belonging to the Thermoguttaceae family within the Pirellulales order of the Planctomycetia class. This study enhances our understanding of Planctomycetota in AD by highlighting their phylogenetic diversity and metabolic capabilities.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gerardo Mejia, Angélica Jara-Servin, Cristóbal Hernández-Álvarez, Luis Romero-Chora, Mariana Peimbert, Rocío Cruz-Ortega, Luis D Alcaraz
{"title":"Rhizosphere microbiome influence on tomato growth under low-nutrient settings.","authors":"Gerardo Mejia, Angélica Jara-Servin, Cristóbal Hernández-Álvarez, Luis Romero-Chora, Mariana Peimbert, Rocío Cruz-Ortega, Luis D Alcaraz","doi":"10.1093/femsec/fiaf019","DOIUrl":"10.1093/femsec/fiaf019","url":null,"abstract":"<p><p>Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesized that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 operational taxonomic units across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (P ≤ .05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into bacteria (93.7%) and eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertilizer use in agriculture.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Diana Masch, François Buscot, Wolfgang Rohe, Kezia Goldmann
{"title":"Bark beetle infestation alters mycobiomes in wood, litter, and soil associated with Norway spruce.","authors":"Diana Masch, François Buscot, Wolfgang Rohe, Kezia Goldmann","doi":"10.1093/femsec/fiaf015","DOIUrl":"10.1093/femsec/fiaf015","url":null,"abstract":"<p><p>Recent exceptionally hot and dry summers provoked massive bark beetle outbreaks in German forests, which killed many conifers, forcing to clear-cut complete non-mature stands. The importance of fungi in ecosystems in particular in association with trees is widely recognized, but the ecology of how insect infestations of trees affect their mycobiomes remains poorly understood. Using Illumina MiSeq sequencing, we investigated fungal communities in soil, litter, and stem wood at early and late stages of bark beetle infestation in a Norway spruce [Picea abies (L.) Karst] stand in Central Germany. Fungal diversity decreased from soil to wood, with the highest proportion of unknown fungi in stem wood. Lifestyles, particularly of those fungi associated with stem wood, clearly changed depending on the infestation stage. The answer of tree-associated fungi to beetle infestation was characterized by an increasing community dissimilarity among all three habitats, i.e. it concerned not only the above-ground fungal communities directly connected to the tree. Our study, thus, pinpoints the cascading effects of tree infestations by bark beetles and subsequent tree diebacks on the proximate and distant mycobiomes of the plant soil system, which should be entirely considered to tackle the effects of environmental events on tree health.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Multi-omics analysis of the correlation between surface microbiome and metabolome in Saccharina latissima (Laminariales, Phaeophyceae).","authors":"Emilie Adouane, Cédric Hubas, Catherine Leblanc, Raphaël Lami, Soizic Prado","doi":"10.1093/femsec/fiae160","DOIUrl":"10.1093/femsec/fiae160","url":null,"abstract":"<p><p>The microbiome of Saccharina latissima, an important brown macroalgal species in Europe, significantly influences its health, fitness, and pathogen resistance. Yet, comprehensive studies on the diversity and function of microbial communities (bacteria, eukaryotes, and fungi) associated with this species are lacking. Using metabarcoding, we investigated the epimicrobiota of S. latissima and correlated microbial diversity with metabolomic patterns (liquid chromatography coupled to tandem mass spectrometry). Specific epibacterial and eukaryotic communities inhabit the S. latissima surface, alongside a core microbiota, while fungal communities show lower and more heterogeneous diversity. Metabolomic analysis revealed a large diversity of mass features, including putatively annotated fatty acids, amino derivatives, amino acids, and naphthofurans. Multiple-factor analysis linked microbial diversity with surface metabolome variations, driven mainly by fungi and bacteria. Two taxa groups were identified: one associated with bacterial consortia and the other with fungal consortia, each correlated with specific metabolites. This study demonstrated a core bacterial and eukaryotic microbiota associated with a core metabolome and highlighted interindividual variations. Annotating the surface metabolome using Natural Products databases suggested numerous metabolites potentially involved in interspecies chemical interactions. Our findings establish a link between microbial community structure and function, identifying two microbial consortia potentially involved in the chemical defense of S. latissima.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tristan E G Biggs, Gonçalo J Piedade, Ella M Wesdorp, Michael P Meredith, Claire Evans, Corina P D Brussaard
{"title":"Temperature-induced changes in the relevance of viral lysis and microzooplankton grazing of Antarctic phytoplankton indicates future alterations in seasonal carbon flow.","authors":"Tristan E G Biggs, Gonçalo J Piedade, Ella M Wesdorp, Michael P Meredith, Claire Evans, Corina P D Brussaard","doi":"10.1093/femsec/fiae158","DOIUrl":"10.1093/femsec/fiae158","url":null,"abstract":"<p><p>Phytoplankton play a pivotal role as the primary producers in polar marine ecosystems. Despite evidence suggesting that production rates and loss factors vary from year to year, and thus drive dynamic ecosystem functioning, interannual comparisons remain sparse. In this study, we examined viral lysis and microzooplankton grazing rates on Antarctic phytoplankton during two productive seasons and compared them with published data from a previous year. Higher rates of phytoplankton gross growth and total mortality during the warmer productive season suggest global warming induced increases in the magnitude of ecosystem carbon flow. Viral lysis rates appear to be relatively independent of average seasonal temperatures, whereas grazing rates were lower during the colder productive seasons (average temperature <0°C). This resulted in a greater relative impact of viral lysis on phytoplankton mortality, particularly pronounced during periods of phytoplankton accumulation. The interannual variations in phytoplankton fate are likely due to a stronger coupling between rates of viral infection and phytoplankton growth compared with grazing. Our results emphasize the importance of monitoring rates of viral lysis, specifically in combination with the size and taxonomy of the phytoplankton community. Collectively these factors determine the relative significance of the different carbon fates, and hence the ocean's efficacy as a carbon sink.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Magda A Rogowska-van der Molen, Alejandro Manzano-Marín, Jelle L Postma, Silvia Coolen, Theo van Alen, Robert S Jansen, Cornelia U Welte
{"title":"From eggs to guts: Symbiotic association of Sodalis nezarae sp. nov. with the Southern green shield bug Nezara viridula.","authors":"Magda A Rogowska-van der Molen, Alejandro Manzano-Marín, Jelle L Postma, Silvia Coolen, Theo van Alen, Robert S Jansen, Cornelia U Welte","doi":"10.1093/femsec/fiaf017","DOIUrl":"10.1093/femsec/fiaf017","url":null,"abstract":"<p><p>Phytophagous insects engage in symbiotic relationships with bacteria that contribute to digestion, nutrient supplementation, and development of the host. The analysis of shield bug microbiomes has been mainly focused on the gut intestinal tract predominantly colonized by Pantoea symbionts and other microbial community members in the gut or other organs have hardly been investigated. In this study, we reveal that the Southern green shield bug Nezara viridula harbours a Sodalis symbiont in several organs, with a notable prevalence in salivary glands, and anterior regions of the midgut. Removing external egg microbiota via sterilization profoundly impacted insect viability but did not disrupt the vertical transmission of Sodalis and Pantoea symbionts. Based on the dominance of Sodalis in testes, we deduce that N. viridula males could be involved in symbiont vertical transmission. Genomic analyses comparing Sodalis species revealed that Sodalis sp. Nvir shares characteristics with both free-living and obligate insect-associated Sodalis spp. Sodalis sp. Nvir also displays genome instability typical of endosymbiont lineages, which suggests ongoing speciation to an obligate endosymbiont. Together, our study reveals that shield bugs harbour unrecognized symbionts that might be paternally transmitted.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143406518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}